Running-in of the main bearings of a diesel engine is a crucial process before service. The running-in period can be divided into several stages, in which different running-in conditions are used. This is termed as multi-stage running-in, which is a good way to enhance running-in quality. In order to reveal the evolution of phase trajectory and compare the running-in quality, the running-in tests were performed with the material of a bearing bush (Sn-11Sb-6Cu) and shaft (AISI 1045). The running-in quality was comprehensively evaluated via friction coefficient, phase trajectory, and surface topography. Results indicate that the phase trajectories show a trend of stage-by-stage convergence. A multi-stage running-in can achieve a more stable attractor, lower friction coefficient and smoother surface, that is, a better running-in quality than the constant running-in scheme. This study provides a reference for formulating running-in specifications for sliding bearings.